Thanks @sabbamitta for bringing all this up. I’ll go through them one by one.
Pācittiya is different because it is offence by definition. Dukkata, by contrast, it a non-technical word that is used throughout the suttas to mean bad conduct. As such it is tricky to distinguish when it refers to an offence and when is merely refers to what is inappropriate. It seems quite likely to me that it initially dukkata always referred to inappropriate conduct that was not technically an offence, and only gradually did it become a separate class of offence, hardly distinguishable from the pācittiyas, thullaccayas, and the dubbhāsitas. This inability to distinguish the offences - in the sense that the penalty is exactly the same - is one of the fingerprints that may indicate that originally only one of these four was an offence. (In other words, why would the Buddha create a number of different classes of offences if there was no difference between them in penalty, confession, or other procedures.)
If you look at the use the word pācittiya in the Pali text, it is always used without āpatti within the rules, but usually with āpatti in the Vibhaṅga commentary. Clearly, it must mean offence in the actual rule, and so it is always appropriate to render it as an offence of pācittiya. Again, pācittiya is word that exclusively refers to offences.
As for segment 95, I am following the punctuation in the Pali, which I think is correct. The point here, I think, is that it is not clear that the Buddha is speaking before the quotation marker. If you look at the text it has a generic feel, with no bhikkhave or other markers that the Buddha is actually speaking. We know the Vibhaṅga has been expanded a long time after the Buddha, and we may be able to distinguish this expansion from the word of the Buddha by carefully distinguishing how the text is presented. At the point you are referring to, suddenly we have bhikkhave, which clearly indicates that the Buddha is speaking again, and so this may mark a more ancient part of the text. (Although as a stand-alone piece of evidence it is obviously not very strong.) So I think it is good to leave the quotation markers, as I believe it accurately reflects the Pali.
As for your comment re. segment 132: I am glad to get such things sorted!